keggtools 0.5.0

Enrichment analysis and visualisation toolkit for KEGG pathways

keggtools

Library for KEGG pathway enrichment analysis.

Installation

keggtools only supports python version greater than or equal 3.6.

Dependencies

• graphviz

python dependencies

• requests
• tqdm
• pydot
• scipy

Installation of python dependencies:

python3 -m pip install requests tqdm pydot scipy

Installation keggtools package using pip:

python3 -m pip install keggtools

To get a more detailed list of install options, please read the INSTALL.md

API

Download and Parsing

from keggtools.resolver import KEGGPathwayResolver
from keggtools.const import IMMUNE_SYSTEM_PATHWAYS

ORGANISM_ID = "hsa"
resolver = KEGGPathwayResolver(org=ORGANISM_ID)

# Select first immune system pathway as example
pathway_id = list(IMMUNE_SYSTEM_PATHWAYS.keys())[1]

# Resolve pathway
pathway = resolver.get_pathway(code=pathway_id)
print(pathway)

Enrichment and Testing

from keggtools.analysis import KEGGPathwayAnalysis

# Init analysis with organism code
analysis = KEGGPathwayAnalysis(org=ORGANISM_ID)

# Study genes as list of entrez gene id's
study_genes = []
analysis.run_analysis(gene_list=study_genes)

# to_dataframe method requires pandas installation
result = analysis.to_dataframe()
print(result.head())

Rendering

import pydot
from keggtools.render import KEGGPathwayRenderer

# Load and parse pathway
pathway = KEGGPathwayResolver(org=ORGANISM_ID).get_pathway(pathway_id)
renderer = KEGGPathwayRenderer(kegg_pathway=pathway)

# Render to dot graph
dot_string = renderer.raw_render()

# Export dot graph as png
graphs = pydot.graph_from_dot_data(dot_string)[0]
graph.write_png("./output.png")

Development

Dev installation

Fast install with virtualenv for development.

python3 -m virtualenv venv
source ./venv/bin/activate
pip install --upgrade pip
pip install -r requirements.txt

Testing

Run unittest to verify keggtools installation

# Install pytest
python3 -m pip install pytest

# Run unittest for package
pytest -p keggtools --show-capture=log

Alternatively, the Makefile can be used:

make unittest

Static code analysis

Static code analysis using mypy

# Install mypy
python3 -m pip install mypy

# Or install full development requirements
pip install -r dev_requirements.txt

Run static code analysis with mypy

mypy setup.py
python3 setup.py install
mypy -p keggtools